VMD Store

[maojinyuan]

Hi, I'm here. Thanks a lot for your help.

The problem of my failure to open VMDware is that it was always loading, I didn't know if my computer has a problem?

BTW, I do the examples as the introduction of molUP, and I get the Gaussian input file and execute it, however, it was repored "MM function not complete" as below, I found the undefined bondstretch and angle bend were exactly the positions of cutten amino acid residues, I wonder this parameters can be added manually or can be added automatically in your package(molUP)? cause I didn't find some related tutorial to avoid this problem.

Include all MM classes Bondstretch undefined between atoms 1209 1211 C-H [H,L] Bondstretch undefined between atoms 2174 2176 C-H [H,L] Bondstretch undefined between atoms 3074 3076 C-H [H,L] Bondstretch undefined between atoms 3864 3866 C-H [H,L] Angle bend undefined between atoms 1202 1209 1211 CT-C-H [H,H,L] Angle bend undefined between atoms 1210 1209 1211 O-C-H [H,H,L] Angle bend undefined between atoms 2167 2174 2176 CT-C-H [H,H,L] Angle bend undefined between atoms 2175 2174 2176 O-C-H [H,H,L] Angle bend undefined between atoms 3066 3074 3076 CT-C-H [H,H,L] Angle bend undefined between atoms 3075 3074 3076 O-C-H [H,H,L] Angle bend undefined between atoms 3851 3864 3866 CT-C-H [H,H,L] Angle bend undefined between atoms 3865 3864 3866 O-C-H [H,H,L] MM function not complete Error termination via Lnk1e in /share/apps/g16.b01/g16/l120.exe at Wed Sep 4 19:21:11 2019.

[henriquefer]

Regarding the VMD Store, can you please show me the content of the "/share/home/maojy/vmd1.9.4a35/vmdStore/vmdStore.rc" file.

---

molUP does not automatically provide additional parameters. When the layers are split between atoms with hydrogens bonded, you have no problem because Gaussian will use the available parameters. For example, consider the following molecule.

  H H
  | |
H-C-C-H
  | |
  H H

If you split the system in two-layer through the C-C bond, Gaussian will not comply about missing parameters because the link-atom is an H and the parameters for that type of bond and angles already exist.

However, if your molecule is something like:

  H F
  | |
H-C-C-Cl
  | |
  H Br

Considering the same two-layer system, the second C does not have parameters for the C-H bond required by the link-atom addition. In this case, you have to provide suitable parameters for the link-atoms.

I hope that this helps you understand the procedure.

In your particular case, you have to identify the atom type of heavy those (e.g. 1209) and add a line on your parameters section:

HrmStr1 CT H 340.00 1.0900

where 340.0 is the force constant and 1.0900 is the equilibrium value.

This also applies to angles bends:

HrmBnd1  C  N  H  50.00 120.0001

[maojinyuan]

This is the content of vmdStore in "/share/home/maojy/vmd1.9.4a35/vmdStore/vmdStore.rc" : vmdStore.txt

vmdStore#### START vmdStore

Version 1.1.11

variable vmdStorePath "/share/home/maojy/vmd1.9.4a35/vmdStore" lappend auto_path $::vmdStorePath vmd_install_extension vmdStore "vmdStore::start" "VMD Store/VMD Store"

vmdStore#### END vmdStore

VMD Store Plugin Manager

Please, do not change this file unless you know what are you doing!

Thank you very much for your help, I'll try the way. 0..0

[henriquefer]

Apparently, the file is okay.

Let me know some other details:

1. Do you have an internet connection active when you start the VMD Store?
2. Send the full VMD output (terminal) after starting VMD Store.

Best regards

[maojinyuan]

Absolutely yes, I am talking to u by Internet. however, I am in China, I wonder if the firewall shield the connect, I have no idea？ Unfortunately，the output in terminal didn't go on, like the picture:

[henriquefer]

Okay. VMD Store only communicates with GitHub, so I suppose that it is not firewall related since you can access GitHub. In fact, the output does not provide any output...

You told me in the other post, that you are running Centos, but this seems to be Windows. Can you confirm the operating system?

[maojinyuan]

I am sorry to reply you so late. Actually, the VMDStore both in Windows and Linux are not work, the picture I uploaded in last answer is the Linux system, I just control it by Xshell.

[henriquefer]

Since we have no idea about the error and before deepening, please remove the vmdStore directory and all the related-lines in the .vmdrc/vmd.rc file. Then, install the VMD Store following tutorial 1. for Window) and 3. for Linux: https://biosim.pt/how-to-install-vmd-store/

[maojinyuan]

Hi, There are some thing I should report to u. I attempt to open the VMDStore in Linux without any changes and it works recent days, but it seem to unstable sometimes, I mean, this time I can load the VMDStore, next time maybe not.

[henriquefer]

Hi, It seems that you are experiencing some kind of instability when the VMD Store tries to communicate with GitHub. I will try to replicate that behavior to try to understand the cause.

[Pharmaoie]

Hi @henriquefer

I am experiencing the same issue with VMDstore not loading.

Here is the error I get when I try to open VMDstore from the extension.

Here is the error message:

invalid command name "styleConfig" invalid command name "styleConfig" while executing "styleConfig ." (procedure "setThemeDefaults" line 12) invoked from within "setThemeDefaults " (procedure "tablelist::handleThemeChangedEvent" line 45) invoked from within "tablelist::handleThemeChangedEvent" ("after" script)

If I choose to skip messages, I get the loading window, and it doesn't go beyond that.

Thanks in advance! -MoSorour

[Ranabirju15]

I am also experiencing the same problem. vmdStore stuck in Loading. I installed vmdStore with VMD for LINUXAMD64, version 1.9.3 in Linux mint OS.